Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add HolobiomicsLab/asb-skill-collections --skill motif-peak-overlap-matchinggit clone --depth 1 https://github.com/HolobiomicsLab/asb-skill-collectionsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/motif-peak-overlap-matching)<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/motif-peak-overlap-matching"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/motif-peak-overlap-matching/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/motif-peak-overlap-matching"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/motif-peak-overlap-matching.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00066 | $0.01458 |
| Opus 5 | $0.00033 | $0.00729 |
| Sonnet 5 | $0.00013 | $0.00292 |
| Haiku 4.5 | $0.00007 | $0.00146 |
Grade A, and why
motif-peak-overlap-matching scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 106 lines — stays where its author put it; the contents beside it link to each section on GitHub.
motif-peak-overlap-matching
Summary
Match transcription factor motifs to chromatin accessibility peaks to identify which peaks contain which DNA binding motifs. This is an essential preprocessing step that links motif occurrence to peak regions before computing deviation scores in chromatin accessibility analysis.
When to use
Apply this skill when you have a filtered set of non-overlapping peaks from ATAC-seq data and a collection of motifs (typically from JASPAR or similar databases), and you need to identify which peaks contain matches to which motifs as a prerequisite for computing motif-based deviation scores across samples.
When NOT to use
- You already have pre-computed motif-peak matches from another tool or database and do not need to re-match.
- Your peaks have not been filtered for quality or overlaps, as matching on unfiltered peak sets may produce spurious or redundant motif calls.
- Your reference genome does not match your peak coordinate system (e.g., peaks are from hg38 but you provide hg19).
Inputs
- motif collection (e.g., JASPAR motifs as PWMatrix or PWMatrixList)
- filtered peaks (GenomicRanges object)
- reference genome (BSgenome object, e.g., BSgenome.Hsapiens.UCSC.hg19)
Outputs
- motif-peak index object (sparse binary matrix or similar structure indicating which peaks contain which motifs)
How to apply
Use the matchMotifs function from the motifmatchr package, providing the motif collection, the filtered peak set as a GenomicRanges object, and a reference genome (e.g., BSgenome.Hsapiens.UCSC.hg19). The function performs sequence matching to determine peak-motif overlaps. The resulting motif-to-peak index object stores which peaks contain which motifs, and this becomes the 'annotations' argument for downstream computeDeviations. The matching is genome-aware: it retrieves sequences from the reference genome corresponding to each peak region and scans for motif matches using position weight matrices, enabling accurate identification of potential transcription factor binding sites.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 106 lines · 66 tokens per session scan A 1dd1daab3961
motif-peak-overlap-matching is a skill published in the GitHub repository HolobiomicsLab/asb-skill-collections (15 stars, last pushed yesterday), licensed Apache-2.0. It adds 66 tokens to every session and 1,458 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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